PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem.

ABSTRACT:

Motivation

Recent advances in single-cell sequencing (SCS) offer an unprecedented insight into tumor emergence and evolution. Principled approaches to tumor phylogeny reconstruction via SCS data are typically based on general computational methods for solving an integer linear program, or a constraint satisfaction program, which, although guaranteeing convergence to the most likely solution, are very slow. Others based on Monte Carlo Markov Chain or alternative heuristics not only offer no such guarantee, but also are not faster in practice. As a result, novel methods that can scale up to handle the size and noise characteristics of emerging SCS data are highly desirable to fully utilize this technology.

Results

We introduce PhISCS-BnB (phylogeny inference using SCS via bran

SUBMITTER: Sadeqi Azer E 

PROVIDER: S-EPMC7355310 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature